What is the function of the Clip option of Quad View?
Like the names says it clips whatever is outside view.

In the case of a quad view, if you pan or move one of the orthographic views (front, top, left or right) whatever goes outside that specific viewport gets clipped or hidden in the other ones (except for perspective views).

If in top view you pan your scene in such way that part of the objects stay out of that viewport, then those objects also get hidden in the other views as well, despite being visible otherwise.